miRNA: 3'- gUAGUCGA---------------AUGAGAGGG-GCAcGGCGG- -5'
miRNA: 3'- -GUAGuCGAa---UGA-GAgGGGcACGGCGG- -5'
miRNA: 3'- -GUAGucGAAUGA-GAGgGGCACGGCGG- -5'
miRNA: 3'- -GUAGUCGAAUGAGAGGGGCACGGCGG- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 956 | 5' | -56 | NC_000902.1 | + | 39241 | 0.66 | 0.724729 |
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Target: 5'- uGUCGGCUauuucaucccgccaaUAUUUUCCCaCGUcCCGUCa -3' miRNA: 3'- gUAGUCGA---------------AUGAGAGGG-GCAcGGCGG- -5' |
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| 956 | 5' | -56 | NC_000902.1 | + | 24085 | 0.66 | 0.677714 |
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Target: 5'- gCAUC-GCUgaccACUuCUgCCC-UGCCGCCa -3' miRNA: 3'- -GUAGuCGAa---UGA-GAgGGGcACGGCGG- -5' |
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| 956 | 5' | -56 | NC_000902.1 | + | 3962 | 0.68 | 0.569126 |
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Target: 5'- gCAUCucUUUGCUgCUCgUCGUGCCGCUg -3' miRNA: 3'- -GUAGucGAAUGA-GAGgGGCACGGCGG- -5' |
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| 956 | 5' | -56 | NC_000902.1 | + | 25556 | 1.11 | 0.000687 |
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Target: 5'- uCAUCAGCUUACUCUCCCCGUGCCGCCu -3' miRNA: 3'- -GUAGUCGAAUGAGAGGGGCACGGCGG- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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